On the public Main Galaxy instance at https://main.g2.bx.psu.edu/(usegalaxy.org), ELANDMULTI format is required for paired-end data, and
there are no conversion tools available if the alignments are performed
with Bowtie.

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A good alternative to try is the public Cistrome Galaxy instance at
http://cistrome.org/ap/. SAM/BAM input for paired-end data is an
accepted in the version of MACS offered there.

I believe the Galaxy Main Tool Shed also has a version of MACS that is
similar to the one at Cistrome, for use in a Cloudman Galaxy, but it is
down right now so I can't double check for you (is just temporary, will
be up soon). But if this interests you, please have a look once up,
likely later today.

Using the Galaxy public server, Is it possible to do peak calling
using MACS on Bowtie mapped paired end reads if I do not have access
to ELAND to generate ELANDMULTI format. The illumina reads were
originally downloaded from the SRA database rather than being
generated in house. Is it possible to convert the Bowtie output to
ELANDMULTI format?

Thanks,
Theresa Murphy

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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/